The main contractor on the new eastern span of the Bay Bridge says Caltrans owes it nearly $50 million — a large chunk of what could add up to $140 million in cost overruns on the project.

Caltrans revealed the demand Thursday from the main contractor, a joint venture called American Bridge/Fluor. Officials did not say what the disputed costs were for, but they acknowledged that the state will probably have to pay at least some of them, depending on the outcome of an expected arbitration process.

“As a risk manager, I need to be conservative in my approach,” said Caltrans official Patrick Treacy, who said he was including the full $49.9 million bill from American Bridge/Fluor in his estimate that the bridge could end up $140 million in the red. “I’m trying to capture the pessimistic outlook.”

Treacy delivered his estimate at a meeting in Oakland of the bridge project’s oversight panel, consisting of the heads of Caltrans, the state Transportation Commission and the local Metropolitan Transportation Commission.

“You’re assuming we basically lose all of our arguments” with American Bridge/Fluor, said Steve Heminger, executive director of the Metropolitan Transportation Commission and a bridge project board member.

“The majority of them, yes,” Treacy said. “To get this, we need a bad result in arbitration.”

American Bridge/Fluor challenged the penalty, and that issue will now be part of the arbitration, said Andrew Fremier, deputy director of the Metropolitan Transportation Commission.

American Bridge/Fluor representatives have not commented about the project, but they have previously defended the quality of the joint venture’s work, and said they would help Caltrans fix the tower rods problem. They did not appear at the meeting Thursday.

Construction delays and environmental protection efforts are contributing to the potential $140 million deficit on the bridge project, which already has cost $6.4 billion. Transportation officials have said there is enough money in toll-payer-financed funds to cover the repairs without having to bump up the cost of driving across Bay Area bridges. Tolls were last raised in 2010.

Heminger expressed frustration that costs continue to escalate, including tens of millions in Caltrans staffing expenses as demolition on the old eastern span and other work continues. He said the panel has tried to cut such costs, without success.

“It’s not making sense to me — that (overhead) number continues to grow every quarter, no matter what we do,” Heminger said.

“We do have issues where there’s a lot of uncertainty about them,” said Treacy, referring to costs for environmental measures to protect nesting birds on the old span and reduce lead contamination in the bay as the structure is dismantled.